inst/doc/Intro_to_ImmuneSpaceR.R

In ImmuneSpaceR: A Thin Wrapper around the ImmuneSpace Database

## ----knitr, echo=FALSE, cache = FALSE-----------------------------------------
library(knitr)
library(rmarkdown)
opts_chunk$set(cache = FALSE, fig.align = "center", fig.width = 7, fig.height = 5)

## ----netrc_req, echo = FALSE--------------------------------------------------
# This chunk is only useful for BioConductor checks and shouldn't affect any other setup
if (!any(file.exists("~/.netrc", "~/_netrc"))) {
    labkey.netrc.file <- ImmuneSpaceR:::.get_env_netrc()
    labkey.url.base <- ImmuneSpaceR:::.get_env_url()
}

## ----CreateConnection, cache=FALSE, message=FALSE-----------------------------
library(ImmuneSpaceR)
sdy269 <- CreateConnection(study = "SDY269")
sdy269

## ----getDataset---------------------------------------------------------------
sdy269$getDataset("hai")

## ----getDataset-filter, message = FALSE---------------------------------------
library(Rlabkey)
myFilter <- makeFilter(c("gender", "EQUAL", "Female"))
hai <- sdy269$getDataset("hai", colFilter = myFilter)

## ----getGEMatrix--------------------------------------------------------------
sdy269$getGEMatrix("SDY269_PBMC_LAIV_Geo")

## ----getGEMatrix-multiple-----------------------------------------------------
sdy269$getGEMatrix(c("SDY269_PBMC_TIV_Geo", "SDY269_PBMC_LAIV_Geo"))

## ----getGEMatrix-summary------------------------------------------------------
gs <- sdy269$getGEMatrix("SDY269_PBMC_TIV_Geo", outputType = "summary", annotation = "latest")

## ----plotting-----------------------------------------------------------------
sdy269$plot("hai")

sdy269$plot("elisa")

## ----cross-connection---------------------------------------------------------
con <- CreateConnection("")

## ----cross-connection-print---------------------------------------------------
con

## ----cross-connection-qplot---------------------------------------------------
plotFilter <- makeFilter(
  c("cohort", "IN", "TIV 2010;TIV Group 2008"),
  c("study_time_collected", "EQUALS", "7")
)
con$plot("elispot", filter = plotFilter)

## ----sessionInfo--------------------------------------------------------------
sessionInfo()